Using wildlife to biomonitor for antimicrobial resistance in the Scottish environment

  • Derek Elsby

Student thesis: Doctoral ThesisDoctor of Philosophy (awarded by UHI)


Antimicrobial resistance (AMR) is a threat to global health. Surveillance of AMR
bacteria in wildlife host is key to understanding and tracking their spread
throughout our environment. We established baseline data on the prevalence of
AMR E. coli in Scottish wild deer, utilising faecal samples gathered from across the country. Using both breakpoint plate (sample level) and published disk-diffusion (isolate level) methods, we found that resistance to tetracycline was the most prevalent phenotype, while resistance to other antimicrobial classes was generally low or not detectable. However, instances of clinical resistance to fluoroquinolones, carbapenems, 3rd gen. cephalosporins, and genes associates with extended spectrum β-lactamase resistance were detected. We also investigated the use of freshwater invertebrates as a biomonitoring tool. We utilised invertebrate samples to obtain reference data on the AMR of E. coli present in the freshwater invertebrate gut, across three distinct river catchments. Using the breakpoint plate method, no significant difference in the prevalence of tetracycline or cefpodoxime resistance was observed between the three catchments. However, isolate based investigation revealed a much broader range of resistance phenotypes in those catchments with greater levels of anthropogenic activity. In isolates from both wild deer and freshwater invertebrates, we observed a population-wide shift in the phenotypic resistance for some antimicrobials, indicating that the use of bespoke cut-off values for the determination of non-wild type isolates would be preferable to published values. Using statistical modelling, we found potential links between the AMR observed in the study populations and livestock, human leisure activities, companion animals and other wildlife.
Date of Award18 Jan 2021
Original languageEnglish
Awarding Institution
  • University of the Highlands and Islands
SponsorsESF studentship & Scottish Funding Council
SupervisorMark Taggart (Supervisor) & Kenny Boyd (Supervisor)

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